Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30066 discussions

Installation Support for Windows (WSL Linux)
by Sabrena Tuy 02 Sep '23

02 Sep '23

External Email - Use Caution Hello, I am a student in an MRI lab at SDSU that uses Freesurfer religiously, and unfortunately, I am a Windows (11) user. I have scrolled mindlessly and have made some progress on beginning the installation for Freesurfer, but I have come to a complete standstill. Is there any way you can help me install the program onto my PC since I will need to use it for my lab work? Sincerely, Sabrena Tuy Sincerely, Sabrena Tuy

1 0

Ubuntu developer password
by Alex Gomez 01 Sep '23

01 Sep '23

External Email - Use Caution Good evening, I appreciate the brevity of your response. This time I got an error with the password of the username: developer that was sent to me to start ubuntu. I could not access the uppercase and lowercase letters. I am writing this email in order to request that password from the username developer. Best regards Alex

1 1

mri_synthmorph
by John Anderson 01 Sep '23

01 Sep '23

External Email - Use Caution Dear Freesurfer experts, I processed DTI data using dt_recon, and I want to register FA images to the standard MNI152 space. However, after running the command mri_synthmorph fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz, the registration is not accurate. I'm not sure what I've done wrong. Thank you for any guidance. sincerely J

2 3

developer password request for VM
by Sharifeh Hoseyni 01 Sep '23

01 Sep '23

External Email - Use Caution Dear FreeSurfer community, I am currently following the instructions on the Free Surfer Wiki to have FreeSurfer on a Windows Computer with VirtualBox However, upon startup of the virtual machine, the Ubuntu installation asks me the password for "developer" user. May I ask you please send me the password? Thanks in advance best regards

1 0

FreeSurfer VirtualBox Password
by Camille Fakche 01 Sep '23

01 Sep '23

External Email - Use Caution Dear FreeSurfer community, I am currently following the instructions on the Free Surfer Wiki to have FreeSurfer on a Windows Computer with VirtualBox ( https://secure-web.cisco.com/1ZtCDHxlGLq6zCZl5MFfo63XxEGZEA9XUghAEwDDA7AHOH…) I need the password to unzip the FS_7_2_0_Ubuntu_18_04_06.ova.7z file, could you send it to me? Thank you for your help, Camille. -- FAKCHE Camille Post Doctoral Researcher Centre for Human Brain Health (CHBH) University of Birmingham, UK

1 0

Error mri_ca_register
by Shamas, Mohamad 01 Sep '23

01 Sep '23

External Email - Use Caution Hello, I am having a problem running Freesurfer on Linux server Centos 7. I installed freesurfer correctly and when I try to run the command: recon -all -s sample -I sample-001.mgz -all I get an error message : mri_ca_register with non-zero status 9 I attached here the log file, I am using version 7.4.1. Can you please help me figure out a solution for the problem. Thanks MShamas ________________________________ UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

2 1

Online Machine Learning School 25th-29th of September!
by Dominic Dwyer 01 Sep '23

01 Sep '23

External Email - Use Caution Join our global Online Machine Learning School from 25th-29th of September! Our hub is in Munich where Prof. Nikolaos Koutsouleris and his team are organizing the school together with the ECNP Neuroimaging Network<https://secure-web.cisco.com/1Q0FlhdtDGhI4WHxL_BSCDIgIHZwPXEgZ-7jlpgcSuSd57…>. This will enable participants to join hands-on tutorials within the Central European Summer Time zone. Register here.<https://secure-web.cisco.com/1BYsTzN1nhmVNzh6r5AoBaSAkpWKFBxVxaXIgDhzpYA7K9…> For the first time, this school is also being conducted in Melbourne by Dr. Dom Dwyer and the Orygen<https://secure-web.cisco.com/1aZHFQk-5Dsi42Di-c8ps6w3mqfwrnj_8R4DnFXmP3azoi…> Youth AI team, supported by The University of Melbourne<https://secure-web.cisco.com/1sxj8NxhZY9uUVdg4iyEjGtPTQ0EcGuVHbxcmn5NF4faXf…> and the PRE-EMPT<https://secure-web.cisco.com/1k4FvOxOJLCojOsS86LCRKoWF7G7zHllWukVfBKmKxKMQY…> project. This school is for participants in Asia-Pacific time zones and we offer tutorials in English, Vietnamese, and Mandarin Chinese. Register here<https://secure-web.cisco.com/1lBX__FRY65kQLCeJ-wlEVb7l0tyf52gSeE2rUEj7vgWMv…>. People with all levels of experience are encouraged to apply because you do not need coding experience to implement the cutting-edge machine learning techniques we teach. The school is tailored to online learning by providing different learning formats, including: * Seminars covering essential concepts * Hands-on tutorials using NeuroMiner<http://secure-web.cisco.com/1e0kasQJFGVzBzsH2XCpQGi7634oTmal96N_CgD6Hd2C37I…> that do not require coding experience * Application of learnt material in a machine learning competition with continuous assistance from tutors * Daily lectures from international experts in the field There are only 100 full course places available in total - so be quick! The school is supported by the Section for Precision Psychiatry (LMU Klinikum)<https://secure-web.cisco.com/1tsLPyg2gGodLtS69Jl8b-LklQ8KsPuhm7a9E6noa_4v19…>, the Max Planck Fellow Group for Precision Psychiatry<https://secure-web.cisco.com/1V2yN_65ALR2c7A7oKS6fBZnSzF3iWUIB_gf3fvav8iP-n…>, the Artificial Intelligence in Mental Health Lab (KCL)<https://secure-web.cisco.com/1GnD6RqYQ0zIwDigj2i14eK0sTQiINppUXPi3V8Gx8KtKl…>, the ECNP<https://secure-web.cisco.com/1Iu8Q5wDp3OgungBbANpPK5lHxoL0sECWxf_ob-uKu5lgv…> and the ECNP Neuroimaging Network<https://secure-web.cisco.com/1cJgS2dFS--j-LLASxoIo4d9dwaW0OAHFrqEpvft0DQSpC…>. It is also supported by Orygen, the University of Melbourne, and the Orygen Data Science and Analytical Methods team. For more information and to register for the school, please see the attached flyer or visit our website at https://secure-web.cisco.com/1BYsTzN1nhmVNzh6r5AoBaSAkpWKFBxVxaXIgDhzpYA7K9…<https://secure-web.cisco.com/1BYsTzN1nhmVNzh6r5AoBaSAkpWKFBxVxaXIgDhzpYA7K9…>. Looking forward to hearing from you! Best wishes, Your Online Machine Learning School Team

1 0

passcode
by Alex Gomez 31 Aug '23

31 Aug '23

External Email - Use Caution Hi, I would like to request the passcode for unzipping the Virtual Box Image file (i.e. FS_7_2_0_ubuntu_18_04_06.ova.7z). Best regards Alex

1 0

Fwd: recon-all error: matlab gives: Unrecognized function or variable 'make_outer_surface'.
by fsbuild 30 Aug '23

30 Aug '23

External Email - Use Caution If you have not already done so, I would try installing and using the newest version of the Matlab runtime environment that the 7.4.1 release was tested with, i.e. R2019b.  Once you have set $FREESURFER_HOME, then run the fs_install_mcr script included with the freesurfer distribution .... $ export FREESURFER_HOME=<your install path> $ cd $FREESURFER_HOME/bin $ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2019b … answer y to any installer questions ... Then I think it should work to find the Matlab libraries by at least start off with setting, $ export LD_LIBRARY_PATH=$FREESURFER_HOME/MCRv97/bin/glnxa64 Please make sure you have otherwise removed from your environment and references to the previous Matlab R2022b setup. - R. Begin forwarded message:From: Benjamin Cole Sherman <bsherma(a)stanford.edu> Subject: [Freesurfer] recon-all error: matlab gives: Unrecognized function or variable 'make_outer_surface'. Date: August 30, 2023 at 12:02:09 EDT To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>         External Email - Use Caution        Hi FreeSurfer Team,I'm trying to run recon-all on an MRI nii.gz file and I believe most of the command runs as the error doesn't happen until several hours in, however once matlab is initiated I consistently get the following output:MATLAB is selecting SOFTWARE OPENGL rendering.                            < M A T L A B (R) >                  Copyright 1984-2022 The MathWorks, Inc.                  R2022b (9.13.0.2049777) 64-bit (glnxa64)                              August 24, 2022Warning: Function iscolumn has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict.Warning: Function ismatrix has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict.Warning: Function isrow has the same name as a MATLAB builtin. We suggest yourename the function to avoid a potential name conflict.Warning: Function narginchk has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict.Warning: Function isequaln has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict.Warning: Function istable has the same name as a MATLAB builtin. We suggest yourename the function to avoid a potential name conflict.Warning: Function isfile has the same name as a MATLAB builtin. We suggest yourename the function to avoid a potential name conflict.Warning: Function isfolder has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict..Warning: Function isstring has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict. For online documentation, see https://secure-web.cisco.com/1A7cHJG7OTQToCpTNsg3ycqt5UEObzYbnyuy3… product information, visit http://secure-web.cisco.com/1PkNE_zNSBM0yzYMjwH_cGeVC4O7UdJdfnli… Unrecognized function or variable 'make_outer_surface'. >> ERROR: make_outer_surface did not create output file '/usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!Command exited with non-zero status 1I haven't been able to find anything in the support archives so I was hoping you could help us out.1)Freesurfer version: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb84602)Platform: Ubuntu 20.04.6 LTS3)recon-all.log: see attachedThanks for any help you can provide!_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

recon-all error: matlab gives: Unrecognized function or variable 'make_outer_surface'.
by Benjamin Cole Sherman 30 Aug '23

30 Aug '23

External Email - Use Caution Hi FreeSurfer Team, I'm trying to run recon-all on an MRI nii.gz file and I believe most of the command runs as the error doesn't happen until several hours in, however once matlab is initiated I consistently get the following output: MATLAB is selecting SOFTWARE OPENGL rendering. < M A T L A B (R) > Copyright 1984-2022 The MathWorks, Inc. R2022b (9.13.0.2049777) 64-bit (glnxa64) August 24, 2022 Warning: Function iscolumn has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function ismatrix has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function isrow has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function narginchk has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function isequaln has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function istable has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function isfile has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function isfolder has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function isstring has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. For online documentation, see https://secure-web.cisco.com/13dZgITxzA846nUba6W_D2_W9PFkrs3ibHMRaWbFXiq0_q… For product information, visit http://secure-web.cisco.com/1wgw042nbZL0hU6HIRu6Xfp7twuvdIG8MKHiB4v2D5d-qKz… >> Unrecognized function or variable 'make_outer_surface'. >> ERROR: make_outer_surface did not create output file '/usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Command exited with non-zero status 1 I haven't been able to find anything in the support archives so I was hoping you could help us out. 1)Freesurfer version: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 2)Platform: Ubuntu 20.04.6 LTS 3)recon-all.log: see attached Thanks for any help you can provide!

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer